tbuckley/cabot-search huggingface dataset:
TMIC-32. TUMOR CELL CILIA ASSOCIATE WITH SPECIFIC IMMUNE CELL POPULATIONS IN HUMAN AND MOUSE MODELS OF GBM
Authors: Loic Deleyrolle, Jeffrey Harrison, Gregory Takacs, Matthew Sarkisian
Journal: Neuro-Oncology (2022)

Abstract INTRODUCTION Glioblastoma (GBM) typically recurs after standard of care therapies. A major obstacle is that GBMs employ various mechanisms to suppress the host immune system, preventing destruction and removal of cancer cells. A better understanding of the crosstalk mechanisms between tumor and immune cell types is needed to advance immunotherapeutic approaches against GBM. GBMs contain primary cilia, organelles likened to both cellular ‘antennae’ and transmitters, and their presence is associated with more aggressive and treatment resistant tumors. OBJECTIVE To explore whether ciliated GBM cells associate with infiltrating immune cells and to determine if these interactions are specific for certain immune cell populations. METHODS We immunostained GBM patient specimens and sections from syngeneic mouse models of GBM for markers of cilia (ARL13B and gTub) together with various immune cell markers (CD45, CD11b, Ly-6B.1, CD3). Cilia were also examined in brain tumors generated in CCR2+/rfp/CX3CR1+/gfp mice, to evaluate the proximity of glioma cell cilia to CCR2- and CX3CR1-expressing myeloid cell subpopulations (brain resident microglia as well as peripheral-derived macrophages and monocyctic- MDSCs (M-MDSCs). Proximity of tumor cell cilia to different markers or cell types was quantified using nearest neighbor analyses. RESULTS In patient samples, CD45+ cells extended processes that contacted the tumor cilia and cilia tip. Similar observations were made in intracranial GBM-bearing mice where we detected juxtaposition of cilia with recruited immune cells (i.e. CD45, CD11b and Ly-6B.1). Notably, cilia predominately associated with immune-suppressive M-MDSCs. Further, CD3+ T cells rarely juxtaposed tumor cilia and maintained greater distances away from ciliated tumor cells compared to M-MDSCs. CONCLUSION Our data suggest specific interactions between ciliated tumor cells and select immune-suppressive cell types, raising the possibility immunologically cold tumors may contain more ciliated cells. Ongoing studies are examining how the tumor immune cell landscape develops depending on the presence of tumor cilia.
NCOG-19. TUMOR INVASION INFLUENCES ON COGNITIVE FUNCTION IN RIGHT CEREBRAL HEMISPHERIC GLIOBLASTOMAS
Authors: Riho Nakajima, Masashi Kinoshita, Hirokazu Okita, Mitsutoshi Nakada
Journal: Neuro-Oncology (2022)

Abstract INTRODUCTION Glioblastoma cells broadly infiltrate into surrounding brain parenchyma. In this study, we investigated the influence of tumor invasion on cognitive function in glioblastomas, using diffusion tensor imaging (DTI) . METHODS Participants were 32 patients with right hemispheric glioblastoma who underwent surgery in Kanazawa University Hospital (mean age, 61.8 years). We evaluated the differences in p-map and q-map, which represent diffusion isotropy and anisotropy with the patients' preoperative DTI. The patients were divided into two groups: less-invasive and highly-invasive types. Following clinical and demographic factors were collected retrospectively: age, sex, volume of enhanced lesion, tumor location, and methylation status of MGMT promoter. Several kinds of cognitive functions mediated by right cerebral hemisphere were assessed preoperatively. All these factors were compared between two groups. Moreover, voxel-based lesion symptom (VLSM) analyses were performed to investigate brain regions relate to decline of cognitive function by tumor invasion. RESULTS All clinical and demographic factors were not significantly different between two groups. Tumor cells significantly infiltrated to insula and basal ganglia in highly-invasive group. Verbal fluency, executive function, attention, and social cognition were impaired in highly-invasive group (p=0.0067, 0.036, 0.0064, and 0.030, respectively). Score of verbal fluency and social cognition were significantly lower when tumor infiltrated to the medial frontal region including cingulate cortex, and deep part of posterior middle and inferior frontal gyrus. Invasion to the sagittal stratum influenced on deterioration of attention and executive function. CONCLUSION The present study revealed that tumor invasion extending beyond the enhanced lesion causes deterioration of cognitive functions such as verbal fluency, executive function, attention, and social cognition in right hemispheric glioblastoma.
TMIC-40. TRANSCRIPTOMIC CHARACTERIZATION OF PATIENT GLIOMAS AND DERIVED MODEL SYSTEMS REVEALS ENVIRONMENTAL INFLUENCE ON NEURODEVELOPMENTAL CELLULAR STATES
Authors: Nicholas Bayley, Christopher Tse, Jenna Minami, Henan Zhu, Weihong Yan, Lynn Baufeld, Laura Gosa, Lisa Ta, William Yong, Robert Prins, Timothy Cloughesy, Linda M Liau, Thomas G Graeber, David Nathanson
Journal: Neuro-Oncology (2022)

Abstract Bulk tumor and single-cell RNA sequencing have revealed the remarkable molecular heterogeneity and plasticity of gliomas, leading to the definition of tumor subtypes and cellular states describing inter- and intra-tumoral levels of heterogeneity respectively. While there has been great interest in creating and revising these classifications, the combination of selective pressures from molecular alterations within the tumor cell as well as extrinsic factors within the tumor microenvironment (TME) driving these levels of heterogeneity remain to be fully described. The brain TME is a complex, regionally heterogeneous ecosystem of communicating non-malignant and malignant cell types and scavenge-able nutrients and metabolites. We hypothesized that distinct environmental contexts within and across tumors may drive the intra- and inter-tumoral heterogeneity of gliomas. To identify tumorigenic programs impacted by environmental context, we performed bulk RNA sequencing of over 40 triplets of patient glioma samples and their matched derivative models established in direct orthotopic mouse xenografts and conventional gliomasphere cultures. Comparative analyses revealed environment-associated programs including in vivo immune and neuroglial signaling as well as altered in vitro lipid metabolism and upregulated cell migration. Next, to investigate associations between tumor cellular state and environment-associated programs we performed single-cell RNA sequencing of 4 patient and model system triplets. By annotating single cell profiles with previously defined single cell atlases of the developing and adult brain, 9 major states reflecting neurodevelopmental cell types were identified. Single cell profiling further revealed cell state-specific expression of environment-associated programs. We simultaneously observed the divergence of model cellular state compositions towards states expressing programs associated with their environment. We conclude that the transcriptional evolution of cellular states is connected to their ecological role within the TME. Consequently, we find grade- and diagnosis-associated composition differences between patient tumors predictive of their ability to establish a model in vitro.
TMIC-20. SERINE AND ONE-CARBON METABOLISM ADAPTING GLIOMA CELLS TO LOW GLUTAMINE MICROENVIRONMENT
Authors: Kazuhiro Tanaka, Hiroaki Nagashima, Hirofumi Iwahashi, Mitsuru Hashiguchi, Takashi Sasayama
Journal: Neuro-Oncology (2022)

Abstract Cancer cells optimize nutrient utilization to supply energetic and biosynthetic pathways. This metabolic process also includes redox maintenance and epigenetic regulation through nucleic acid and protein methylation, which enhance tumorigenicity and clinical resistance. However, less is known about how cancer cells exhibit metabolic flexibility to sustain cell growth and survival from low nutrient microenvironment. Here, we find that serine and glycine levels were higher in low-nutrient regions of tumors in glioblastoma multiforme (GBM) patients than they were in other regions. Metabolic and functional studies in malignant glioma cells demonstrated that serine availability and one-carbon metabolism support glioma cell survival following glutamine deprivation. Serine synthesis was mediated through autophagy rather than glycolysis. Gene expression analysis identified upregulation of methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) to regulate one-carbon metabolism in malignant glioma cells and GBM patient-derived sphere cells. In clinical samples, MTHFD2 expression was highest in the nutrient-poor areas around “pseudopalisading necrosis.” Genetic and pharmacological suppression of MTHFD2 caused tumor cell death and growth inhibition of glioma cells upon glutamine deprivation as well as autophagy inhibition did. These results may have important implications for serine-dependent one-carbon metabolism for glioma cells to survive glutamine starvation and suggest a new therapeutic strategy for patients with malignant glioma.
MODL-35. A NOVEL PATIENT-DERIVED TUMOR ORGANOID MODEL IDENTIFIES HDACI PANOBINOSTAT AS HIGHLY EFFECTIVE DRUG IN MENINGIOMAS
Authors: Gerhard Jungwirth, Junguo Cao, Rolf Warta, Mahmoud Moustafa, Amir Abdollahi, Unterberg Andreas, Christel Herold-Mende
Journal: Neuro-Oncology (2022)

Abstract Tumor-organoids (TOs) are novel, complex three-dimensional ex vivo tissue cultures that under optimal conditions accurately reflect the genotype and phenotype of the original tissue with preserved cellular heterogeneity and morphology. They offer a new and exciting platform for studying cancer biology and directing personalized therapies. Our study aimed to establish TOs from meningioma (MGM) and explore drug responses of selected drugs.TOs were established by controlled reaggregation of freshly prepared single-cell suspension of MGM tissue samples in 384-well plates. We were capable of forming several hundred TO equal in size with a success rate of 98%. TOs consisted of largely viable cells, whereas dead cells were predominantly found outside of the organoid. H&amp;E and IF stainings confirmed the successful establishment of dense tissue-like structures. On the molecular level, transcriptional and mutational profiles were conserved in TOs. To query the suitability and reliability of TOs for robust large-scale drug testing by employing nine highly potent compounds, derived from a drug screening performed on MGM cell lines. In total, standardized TOs from 60 patients were formed, including eight grade II and three grade III MGMs. The FDA-approved epigenetic drug panobinostat demonstrated high anti-meningioma effects in the majority of patients. The efficacy was mediated through inhibition of HDAC1/2 validated by siRNA-mediated knockdown experiments. In an orthotopic in vivo model, treatment with panobinostat extended the median survival of mice, however, the therapy was not curative. To further investigate HDACi resistance, transcriptomes of sensitive and resistant TOs were compared. In resistant tumors, a significant induction of the TGFβ pathway was observed.Taken together, we developed a protocol to generate standardized TO from MGM and preserved histological and molecular features of parental tumor. Drug screening of selected drugs in TOs from 60 patients identified HDACi panobinostat as effective drug through inhibition of HDAC1/2.
NIMG-82. RADIOGENOMIC SIGNATURES OF KEY DRIVER GENES IN GBM REVEAL MOLECULAR HETEROGENEITY OF THE TUMOR MICROENVIRONMENT LINKED TO SPATIAL DISTRIBUTION: IMPACT ON THE TRAJECTORY OF GLIOMA EVOLUTION
Authors: Anahita Fathi Kazerooni, Hamed Akbari, Erik Toorens, Dimitris Grigoriadis, Xiaoju Hu, Chiharu Sako, Elizabeth Mamourian, Stephen Bagley, Zev A Binder, Robert Lustig, Steven Brem, Donald O'Rourke, Tapan Ganguly, Subhajyoti De, Artemis Hatzigeorgiou, Spyridon Bakas, MacLean Nasrallah, Christos Davatzikos
Journal: Neuro-Oncology (2022)

Abstract Somatic genomic alterations acquired during GBM growth enhance adaptation of tumor cells to their microenvironment and give rise to molecular heterogeneity. Radiogenomics could facilitate exploration of the underlying pathobiology of tumor growth in specific microenvironments and thereby, promote precision medicine for the patients. We derived radiogenomic signatures of key driver genes and evaluated molecular compositions of tumor groups with predisposition to specific brain regions. Pre-operative multiparametric conventional MRI scans of 357 IDH-wildtype GBM patients with available targeted NGS data were jointly segmented and registered into a common template. We constructed spatial distribution atlases for tumors harboring mutations in driver genes and identified four distinct groups of tumor locations with predilection to the left frontal cingulate region (Group1), right temporal (Group2), right parietal (Group3), and occipital pole (Group4). Evaluation of the differences in molecular features of the tumor groups included: (1) exploring similarities of genomic profiles across all four groups by evaluating cosine similarity metric (CSM) between mutational signatures; (2) quantification of molecular heterogeneity based on Mutant Allele Tumor Heterogeneity (MATH) scores; and (3) inference of the evolutionary trajectories. Groups 1 and 4 were the most different, and Groups 2 and 3 were the most similar tumors, molecularly. The mutational signatures between Groups 1 and 4 revealed a CSM of 0.35. Group1 showed significantly lower MATH score (less heterogeneity) compared to Group4 (p&amp;lt; 0.05). Evaluation of evolutionary patterns suggested NF1 mutation as an early event in Group1, without subsequent gain of function or mutation in EGFR. In contrast, in Group4, EGFR mutations were early events triggering PTEN mutations later in the evolutionary trajectory. Radiogenomic signatures revealed distinct molecular underpinnings for the tumors with predilection towards specific brain regions that may suggest existence of different tumor microenvironments in different brain regions that cause intra- and inter-patient heterogeneity in the molecular tumor composition.
MODL-25. ANALYSIS OF TUMOR CELL HETEROGENEITY IN A HUMAN NEURAL PROGENITOR-BASED MODEL OF GLIOBLASTOMA REVEALS NEURODEVELOPMENTAL PROGRAMS AND CYTOSKELETAL DYNAMICS
Authors: Patrick DeSouza, Xuan Qu, Matthew Ishahak, Colin McCornack, Devi Annamalai, Luis Batista, Ting Wang, Christopher Maher, Jeffrey Millman, Albert Kim
Journal: Neuro-Oncology (2022)

Abstract Glioblastoma (GBM) is the most common primary malignant neoplasm with poor survival despite treatment. Developing effective therapies remains challenging due to intratumoral heterogeneity, which drives therapeutic resistance and recurrence. To understand how genetic events alter the epigenome to enhance clonal fitness, we developed an isogenic human neural progenitor cell (NPC)-based model of the proneural (PRO) GBM subtype. We introduced TERT promoter (TERTp) C228T and gain-of-function TP53 R248Q mutations in H1 human embryonic stem cells. Wildtype (WT) cells, single TERTp, and double TERTp/TP53 mutants underwent differentiation to NPCs. Lentiviral transduction of double mutants with PDGFRA D842V resulted in triple mutant PRO NPCs. Bulk and single cell transcriptomics of our model system revealed hundreds of gene expression changes with increased mesoderm and human GBM mesenchymal (MES) subtype signatures in single TERTp and double TERTp/TP53 mutants, versus WT cells. TERTp mutation increased telomerase expression and activity, conferring proliferative advantage and immortalization in NPCs and astrocytes. Additionally, TERT expression was further increased in TERTp/TP53 mutants. Surprisingly, triple mutant PRO NPCs, versus WT, displayed &amp;lt; 100 differentially expressed genes, associated with neurodevelopmental and dynamic cytoskeletal processes. Evolution analyses using gene counts signature and splicing dynamics revealed a developmental trajectory model from WT to additive mutants to PRO NPCs. Only triple mutant PRO NPCs formed tumors after intracranial injection in athymic nude mice, with mean survival of 100 days. Tumors presented histopathological features of GBM, and single cell transcriptomic analyses revealed evolution from immune-interacting to both neural progenitor- and neuronal-like subpopulations, with similar cell cycling signatures. Transcription factor genes related to WNT signaling and lineage commitment as well as glial and neuronal cytoskeletal genes exhibited epigenetic selection in vivo, signatures also observed in PRO NPCs in vitro. Our model thus provides opportunity for dissection of epigenetic and functional mechanisms underlying serial mutations during PRO tumor evolution.
NCMP-13. TOLERANCE OF HIGH-DOSE METHOTREXATE TREATMENT OF PRIMARY CENTRAL NERVOUS SYSTEM LYMPHOMA (PCNSL) PATIENTS WITH RENAL IMPAIRMENT, CASE SERIES AND REVIEW OF LITERATURE
Authors: Jay-Jiguang Zhu, Luis Chinea, Juan Carlos Rodriguez Quintero, Cornelius Ware
Journal: Neuro-Oncology (2022)

Abstract PCNSL in immune competent patients is a rare extra-nodal non-Hodgkin lymphoma that accounts for 3–4% of newly diagnosed CNS tumors. Treatment consists of high-dose methotrexate (HD-MTX) based polychemotherapy regimen with or without brain radiation. There are few reported cases supporting the use of HD-MTX as a treatment option in such patients with impaired renal function. The objective of this study was to analyze outcomes and tolerance of HD-MTX based chemotherapy regimen (HD-MTX, rituximab and temozolomide, MRT) in patients with PCNSL and renal impairment. We present five patients with median age 63 (range 40 – 67) at diagnosis, with varying degrees of renal impairments, were all treated with and tolerated well of MRT. They are all alive and have been on observation. Cases 2 &amp; 3 had a one functioning kidney and achieved complete responses (CR) without toxicities. Case 1, with history of grade 3 renal insufficiency during his initial HD-MTX and received carboxypeptidase G2 rescue, tolerated re-treatment with MRT at PCNSL recurrence and achieved a partial response (PR) that has been stable for 44 months. Case 4, who had a cadaver-transplanted kidney, was able to get a CR after 8 treatment with MRT. Case 5, with grade 3 chronic kidney disease from type II diabetes mellitus, achieved CR with MRT with slowing down of his MTX clearance. Literature review for reports with PCNSL and renal impairment treated with HD-MTX through March 31, 2022 identified eight cases and their responses and adverse effects summarized. Due to the low number of published cases and limitation of a retrospective analysis, it is impossible to draw a conclusion on the impact of impaired renal function on the tolerance of HD-MTX treatment of PCNSL. However, our findings indicate that a subset of the patients may still benefit from treatment with HD-MTX based chemotherapy.
TMIC-38. CD39 EXPRESSION IN GLIOBLASTOMA TUMOR MICROENVIRONMENT DOES NOT AFFECT SURVIVAL OR T-CELL EXHAUSTION
Authors: Allison Zheng, Ananya Pappu, Sabraj Gill, Isabella Stelter, Manish Aghi
Journal: Neuro-Oncology (2022)

Abstract Glioblastoma (GBM) is the most common malignant brain tumor with a median survival of 15 months. GBM is very difficult to treat due to numerous factors, including the paucity of immune infiltration of the tumor itself. Efforts to overcome this have led to use of immune checkpoint inhibitors such as PD-1 inhibitor, which have revolutionized treatment of many other solid tumors, and yet have not been successful in the treatment of GBM. This has led to many studies investigating various other similar markers. One such marker is CD39, which is highly upregulated in GBM and functions as the first enzyme in the metabolic pathway of ATP breakdown to adenosine. Additionally, CD39 is thought to contribute to T-cell exhaustion. Like PD-1, CD39 inhibition has had preliminary success in the treatment of other solid tumors. However, when tested on GBM, blocking the ATP breakdown pathway did not improve survival in mice, even in conjunction with PD-1 inhibition. Our team sought to determine if the expression of CD39 on the cell surface functioned as an exhaustion marker by injecting two different cell lines of GBM into CD39 global null mice. There was no survival benefit seen in either cell line when compared to wild type mice. Next, expression of known exhaustion markers such as PD-1, TIM3, and LAG3 on tumor infiltrating lymphocytes were analyzed. Expression of TIM3 and 2B4 were found to be increased in CD39KO mice in comparison to wild type (p &amp;lt; 0.01). Additionally, numerous exhaustion markers such as LAG3, TIGIT, and CTLA4 were decreased on tumor in comparison to peripheral blood (p &amp;lt; 0.01). These results demonstrate the complex nature of immune signaling in GBM tumor microenvironment that our team continues to investigate.
TMIC-24. SINGLE-CELL ANALYSIS OF TUMOR-ASSOCIATED MICROGLIA AND MACROPHAGES FROM HUMAN GLIOBLASTOMA
Authors: Atul Anand, Rikke Frydendahl Sick Olsen, Mark Burton, Dylan Scott Lykke Harwood, Frantz Rom Poulsen, Bo Halle, Christian Bonde Pedersen, Torben Kruse, Mads Thomassen, Bjarne Winther Kristensen
Journal: Neuro-Oncology (2022)

Abstract INTRODUCTION Patients with glioblastoma have a very poor prognosis. Tumor-associated microglia and macrophages (TAMs) constitute up to 30 % of the cells in glioblastoma, and they secrete cytokines, chemokines and growth factors that influence the microenvironment. The existence of different TAM subtypes appears to be more complex than the established M1 and M2 phenotypes, but their role in glioblastoma is not fully understood and rarely considered therapeutically. This could explain why many clinical trials fail despite of promising preclinical results. This project aims to interrogate the existence and characteristics of different TAM subtypes in human glioblastoma in order to identify novel subpopulations and therapeutic targets. MATERIALS AND METHODS Live CD11b+ TAMs were isolated from patient glioblastoma tissue, and single-cell RNA sequencing (scRNA-seq) was performed using the 10X Genomics Chromium platform. The data was processed and analyzed with the R-package Seurat. RESULTS We have sequenced 74,000 TAMs/microglia from three glioblastomas and two control brain biopsies. In the controls, we detected mostly microglia, while the primary glioblastomas showed a predominance of monocyte-derived TAMs. We identified 11 TAM subtypes, such as hypoxic, proliferating, interferon-induced, chemokine-producing and TNF-producing TAMs, as well as a novel subtype potentially involved in tumor progression. CONCLUSION AND PERSPECTIVES We have detected a spectrum of TAM subtypes, which is more complex than the established M1 and M2 phenotypes. Our findings confirm a recent TAM scRNA-seq study, and in addition, we identify a novel subpopulation, which express known tumor-promoting genes, normally expressed by cancer cells. We are currently validating our findings. This study contributes to the elucidation of the glioblastoma microenvironment. It will potentially lead to identification of novel clinically relevant targets affecting the TAM-glioblastoma interactions.